The plots of the estimated Rt in the most recent weeks show reasonably stable values despite the gradual relaxation of pandemic mitigation measures, with each region experiencing a very gradual increase. The one exception is NW where we estimate a large increase in Rt from 0.8 in mid-April to 1.3 in mid-May coinciding with the emergence of the Delta variant. Current levels of incidence were last seen during the growing phase of the pandemic at the end of September and will, consequently, require careful monitoring.
From the end of March onwards, the incidence of deaths has continued to fall more sharply than predicted by the model, which is now suggesting a gradual rise over the coming few weeks. This implies that the ONS estimates and the data on deaths are giving contradictory signals and model development is ongoing to try and account for this discrepancy.
The plot of the infection fatality rate (IFR) presents age-specific probabilities of death given infection. It shows an increasing mortality risk from September onwards in all ages until the immunisation programme begins to have an impact in late January. From the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop measures the benefits of immunisation against death over and above the benefits against infection. Specifically, there is an estimated fall to a still-high 3.3% in the over-75s and 0.14% overall. The overall impact of the immunisation programme can be seen more clearly in the ‘All Ages’ plot, where the precipitous decline in IFR since late January is a product of this efficacy against death but also of the increasing proportion of infections in young people; older age groups are immunised and become protected against infection. The impact of the second immunisation doses (initially in the 45-64) becoming widespread will begin to affect this quantity over the coming weeks.
For context, alongside the data used here, other indicators (e.g. hospital admissions, reported new positive tests) are suggesting a resurgent epidemic, largely due to the increasing presence of the Delta strain. Prevalence of infection, as estimated by the ONS Coronavirus Infections Survey, is close to 0.20% in England, though there is large regional heterogeneity with a plateau and perhaps even a slight down-turn in many regions. As we consider the lifting of social-distancing measures, the proximity of Rt to 1 indicates that the epidemic could display a range of qualitative behaviours over the coming period. The next couple of weeks will be crucial. We will continue to monitor the situation closely.
Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.
We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.
We use:
Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).
Value of \(R_t\), the average number of secondary infections due to a typical infection today.
The percentage of a given group that has been infected.
NB: negative growth rates are rates of decline. Values are daily changes.
| Region | Median | 95% CrI (lower) | 95% CrI (upper) |
|---|---|---|---|
| England | 0.03 | 0.02 | 0.04 |
| East of England | 0.01 | -0.02 | 0.03 |
| East Midlands | 0.02 | 0.00 | 0.04 |
| London | 0.02 | 0.00 | 0.04 |
| North East | 0.01 | -0.02 | 0.04 |
| North West | 0.05 | 0.03 | 0.07 |
| South East | 0.01 | -0.01 | 0.04 |
| South West | 0.02 | -0.01 | 0.04 |
| West Midlands | 0.01 | -0.01 | 0.04 |
| Yorkshire and The Humber | 0.01 | -0.02 | 0.03 |
Halving times in days, if a region shows growth than value will be NA.
| Region | Median | 95% CrI (lower) | 95% CrI (upper) |
|---|---|---|---|
| England | NA | NA | NA |
| East of England | NA | 38.00 | NA |
| East Midlands | NA | 361.96 | NA |
| London | NA | 231.40 | NA |
| North East | NA | 42.86 | NA |
| North West | NA | NA | NA |
| South East | NA | 52.77 | NA |
| South West | NA | 63.33 | NA |
| West Midlands | NA | 46.46 | NA |
| Yorkshire and The Humber | NA | 41.23 | NA |
Doubling times in days, if a region shows decline then the value will be NA.
| Region | Median | 95% CrI (lower) | 95% CrI (upper) |
|---|---|---|---|
| England | 24.56 | 17.44 | 40.62 |
| East of England | 79.02 | 20.61 | NA |
| East Midlands | 31.75 | 16.27 | NA |
| London | 30.85 | 16.17 | NA |
| North East | 63.65 | 17.97 | NA |
| North West | 14.57 | 10.52 | 26.80 |
| South East | 57.78 | 17.99 | NA |
| South West | 36.80 | 16.56 | NA |
| West Midlands | 54.84 | 17.07 | NA |
| Yorkshire and The Humber | 85.71 | 21.86 | NA |
NB: negative growth rates are rates of decline. Values are daily changes.
| Region | Median | 95% CrI (lower) | 95% CrI (upper) |
|---|---|---|---|
| England | 0.03 | 0.02 | 0.04 |
| East of England | 0.01 | -0.01 | 0.04 |
| East Midlands | 0.02 | 0.00 | 0.05 |
| London | 0.02 | 0.00 | 0.05 |
| North East | 0.02 | -0.01 | 0.04 |
| North West | 0.06 | 0.03 | 0.08 |
| South East | 0.01 | -0.01 | 0.04 |
| South West | 0.02 | -0.01 | 0.05 |
| West Midlands | 0.01 | -0.01 | 0.04 |
| Yorkshire and The Humber | 0.01 | -0.01 | 0.03 |
Halving times in days, if a region shows growth than value will be NA.
| Region | Median | 95% CrI (lower) | 95% CrI (upper) |
|---|---|---|---|
| England | NA | NA | NA |
| East of England | NA | 71.02 | NA |
| East Midlands | NA | NA | NA |
| London | NA | NA | NA |
| North East | NA | 83.67 | NA |
| North West | NA | NA | NA |
| South East | NA | 80.81 | NA |
| South West | NA | 134.54 | NA |
| West Midlands | NA | 82.02 | NA |
| Yorkshire and The Humber | NA | 70.46 | NA |
Doubling times in days, if a region shows decline then the value will be NA.
| Region | Median | 95% CrI (lower) | 95% CrI (upper) |
|---|---|---|---|
| England | 25.23 | 18.70 | 37.35 |
| East of England | 56.34 | 19.21 | NA |
| East Midlands | 28.88 | 14.76 | 321.77 |
| London | 27.98 | 14.47 | 210.26 |
| North East | 45.11 | 17.24 | NA |
| North West | 12.13 | 8.65 | 19.82 |
| South East | 51.93 | 18.56 | NA |
| South West | 34.26 | 14.84 | NA |
| West Midlands | 46.30 | 17.08 | NA |
| Yorkshire and The Humber | 61.07 | 19.99 | NA |
The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (11 Jun).
The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.
Copyright © MRC Biostatistics Unit, University of Cambridge